For the Sequal if they really wanted to a REAL twist they would have the initial alien's reason for taking over and strip mining earth be that they were the last of their kind on their giant city ship and they were moving from system to system, trying to stay ahead of an even worse baddie.
You would have the giant city ship only moving at a small fraction of the speed of light and their plan was to take over earth, resupply their city ship using our resources and manpower (which would take around 15 years), then get the hell out of here before the really nasty guys show up.
We kinda screwed that plan up and now we have to face the really nasty badass aliens they were running from! Add to that one of the invasion ships survived in south America and has taken over a large portion of brazil and in the sequal we have to work with them after years of fighting them to repel the even worse bad guys!
How is that idea?